Version Compatibility

Reference examples tested with: Ensembl VEP 111+, SnpEff 5.2+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Tumor Mutational Burden

"Calculate TMB from my tumor sequencing data" → Compute tumor mutational burden as nonsynonymous coding mutations per megabase with proper panel normalization for immunotherapy eligibility assessment.

• Python: cyvcf2 for VCF parsing + variant counting per panel region

TMB Calculation from VCF (Ensembl VEP 111+)

Goal: Calculate tumor mutational burden as nonsynonymous coding mutations per megabase from a somatic VCF.